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Mining Genes Related to Single Fruit Weight of Peach (Prunus persica) Based on WGCNA and GSEA

Single fruit weight is an important goal of crop production and horticultural species domestication, but its genetic mechanism is still unclear. In this study, the fruits of different peach fruit types in their first rapid development period were used as materials. First, the differentially expressed genes were analyzed by RNA-seq data. Secondly, weighted gene co-expression network analysis (WGCNA) was used to calculate the correlation between genes and modules, the genes with different expression patterns were divided into 17 modules, the modules were correlated with the phenotype of single fruit, and a highly correlated blue module was obtained. Then, the possible differentially expressed genes and signal pathways among different fruit types were compared by gene set enrichment analysis (GSEA) and 43 significant pathways were obtained. Finally, 54 genes found to be repeatedly expressed in 3 of the methods were screened, and 11 genes involved in plant hormone signal transduction were selected for subsequent analysis according to their functional annotations. Combined with the changing trend of phenotype, three genes (Prupe.7G234800, Prupe.8G079200 and Prupe.8G082100) were obtained as candidate genes for single fruit weight traits. All three genes are involved in auxin signal transduction, with auxin playing an important role in plant growth and development. This discovery provides a new perspective for revealing the genetic law of single fruit weight in peach.

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Physiological Characteristics and Transcriptome Analysis of Exogenous Brassinosteroid-Treated Kiwifruit.

Brassinosteroids (BRs) play pivotal roles in improving plant stress tolerance. To investigate the mechanism of BR regulation of salt tolerance in kiwifruit, we used 'Hongyang' kiwifruit as the test material. We exposed the plants to 150 mmol/L NaCl stress and irrigated them with exogenous BR (2,4-epibrassinolide). The phenotypic analysis showed that salt stress significantly inhibited photosynthesis in kiwifruit, leading to a significant increase in the H2O2 content of leaves and roots and a significant increase in Na+/K+, resulting in oxidative damage and an ion imbalance. BR treatment resulted in enhanced photosynthesis, reduced H2O2 content, and reduced Na+/K+ in leaves, alleviating the salt stress injury. Furthermore, transcriptome enrichment analysis showed that the differentially expressed genes (DEGs) related to BR treatment are involved in pathways such as starch and sucrose metabolism, pentose and glucuronate interconversions, and plant hormone signal transduction, among others. Among the DEGs involved in plant hormone signal transduction, those with the highest expression were involved in abscisic acid signal transduction. Moreover, there was a significant increase in the expression of the AcHKT1 gene, which regulates ion transduction, and the antioxidant enzyme AcFSD2 gene, which is a key gene for improving salt tolerance. The data suggest that BRs can improve salt tolerance by regulating ion homeostasis and reducing oxidative stress.

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Developmental stages and episode-specific regulatory genes in andromonoecious melon flower development.

Given the lack of specific studies on floral development in melon (Cucumis melo L.), we carried out an extensive study involving morphological and transcriptomic analyses to characterize floral development in this species. Using an andromonoecious line, we analyzed the development of floral buds in male and hermaphrodite flowers with both light microscopy and scanning electron microscopy. Based on flower lengths, we established a correlation between the developmental stages and four main episodes of floral development and conducted an extensive RNA-Seq analysis of these episodes. We identified 12 stages of floral development, from the appearance of the floral meristems to anthesis. The main structural differences between male and hermaphrodite flowers appeared between stages 6 and 7; later stages of development leading to the formation of organs and structures in both types of flowers were also described. We analysed the gene expression patterns of the four episodes in flower development to find the genes that were specific to each given episode. Among others, we identified genes that defined the passage from one episode to the next according to the ABCDE model of floral development. This work combines a detailed morphological analysis and a comprehensive transcriptomic study that allows for the characterization of the structural and molecular mechanisms that determine the floral development of an andromonoecious genotype in melon. Taken together, our results provide a first insight into gene regulation networks in melon floral development that are critical for flowering and pollen formation, highlighting potential targets for genetic manipulation to improve crop yield of melon in the future.

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Identification of an Aux/IAA regulator for flesh firmness using combined GWAS and bulked segregant RNA-Seq analysis in watermelon

Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit flesh. Among various quality factors, fruit flesh firmness is a crucial quality parameter influencing the fruit texture, shelf life and its commercial value. The auxin/indole-3-acetic acid (Aux/IAA) plays a significant role in fruit development and ripening of non-climacteric fruits. However, the regulatory mechanism of Aux/IAA in controlling fruit flesh firmness and ripening in watermelon remains unknown. In this study, we employed an integrative approach combining genome-wide association study (GWAS) and bulked segregant RNA-Seq analysis (BSR-Seq) to identify an overlapping candidate region between 12776310 and 12968331 bp on chromosome 6, underlying an auxin-responsive gene (Aux/IAA) associated with flesh firmness in watermelon. Transcriptome analysis, followed by real-time quantitative reverse transcription PCR (qRT-PCR), confirmed that the expression of Aux/IAA was consistently higher in fruits with high flesh firmness. The sequence alignment revealed a single base mutation in the coding region of Aux/IAA. Furthermore, the concomitant Kompetitive/Competitive allele-specific PCR (KASP) genotyping data sets for F2 population and germplasm accessions identified Aux/IAA as a strong candidate gene associated with flesh firmness. Aux/IAA was enriched in the plant hormone signal transduction pathway, involving cell enlargement and leading to low flesh firmness. We determined the higher accumulation of abscisic acid (ABA) in fruits with low flesh firmness than hard flesh. Moreover, overexpression of Aux/IAA induced higher flesh firmness with an increased number of fruit flesh cells while reducing ABA content and flesh cell sizes. Additionally, the allelic variation in Aux/IAA for soft flesh firmness was found to exist in Citrullus mucosospermus and gradually fixed into Citrullus lanatus during domestication, indicating that soft flesh firmness was a domesticated trait. These findings significantly enhanced our understanding of watermelon fruit flesh firmness and consequently the watermelon fruit quality.

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Effects of Exogenous 24-Epibrassinolide Leaves Spraying Application on Chlorophyll Accumulation and Gene Expression Profiles of Chlorophyll Metabolism in Celery

Celery is an important leaf vegetable crop in Apiaceae, of which the petiole and leaf blade are the main edible parts. The content and proportion of photosynthetic pigments, mainly chlorophyll, have an important effect on the growth and quality of celery. As a brassinosteroid (BR) plant hormone with high physiological activity, 24-epibrassinolide (24-EBL) has the physiological functions of promoting chlorophyll accumulation and delaying leaf senescence. To investigate the effects of 24-EBL treatment on chlorophyll accumulation at different growth stages of celery, celery plants (variety Ningqin NO. 1) were treated from 45~59 days after sowing (DAS), at intervals of 7 days, with two different concentrations of 24-EBL: 1.04 × 10−6 mol·L−1 and 1.67 × 10−6 mol·L−1. The content of chlorophyll and the expression levels of genes related to its metabolism were determined in celery leaf blades and petioles at three different stages (52, 59, 66 DAS). In the first stage (52 DAS), 1.04 × 10−6 mol·L−1 treatment of 24-EBL increased the expression levels of genes related to chlorophyll biosynthesis (AgHEML, AgCHLG, and AgCAO) to promote the accumulation of chlorophyll in leaf blades. During the second and third stages (59 and 66 DAS, respectively), 1.67 × 10−6 mol·L−1 24-EBL treatment induced the expression levels of genes related to chlorophyll cyclic regeneration (AgCLH) and inhibited the up-regulation of genes related to chlorophyll degradation (AgNYC, AgHCAR, and AgPPH) to promote chlorophyll (especially chlorophyll b) accumulation. These treatments regulated the ratio of chlorophyll a content to chlorophyll b content and changed the leaf color of the celery. The results show that leaf spraying with an appropriate concentration of 24-EBL can facilitate chlorophyll synthesis by promoting chlorophyll synthesis and cycling-related gene expression levels and increase chlorophyll content in the leaves of celery. This study provides a reference for exploring the specific function of 24-EBL in regulating chlorophyll content during the growth and development of celery.

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Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes.

The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.

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Establishment and application of a Multiple nucleotide polymorphism molecular identification system for grape cultivars

Grapes (Vitis L.) are one of the most important and popular fruits in China. However, efficient identification of grapes is important in the protection of domestic grapes and breeders’ rights. Here, we developed a new method called multiple nucleotide polymorphisms (MNP), which combines the advantages of multiple PCR amplification and high-throughput sequencing to improve the efficiency of grape variety identification. We identified 582 universal MNP markers and screened them based on the whole genome sequencing data of 31 representative cultivars. Subsequently, MNP libraries of 60 common cultivars were constructed using multiple PCR amplification and sequencing. The pairing comparison of 60 grape materials revealed a high identification rate (>99 %) of MNP markers. Furthermore, MNP accurately distinguishes diploid and polyploid, which can assist in molecular identification of grapes. Overall, MNP molecular identification technology provides a new way for grape variety identification. Compared with SNP, MNP reduces the cost of identification because it does not need to make expensive gene chips. In addition, MNP can perform the amplification of thousands of primers in a single tube and uses sequencing instead of polyacrylamide gel electrophoresis, which greatly saves experimental consumables and labor compared with SSR. Collectively, the developed technique has the advantages of low cost and high efficiency, which is more competitive than other identification methods at present. The developed technology can assist in resource research and promote plant breeding.

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Sweet cherry AP2/ERF transcription factor, PavRAV2, negatively modulates fruit size by directly repressing PavKLUH expression.

For sweet cherry, fruit size is one of the main targets in breeding programs owing to the high market value of larger fruits. KLUH/CYP78A5 is an important regulator of seed/fruit size in several plant species, but its molecular mechanism is largely unknown. In this study, we characterized the function of PavKLUH in the regulation of sweet cherry fruit size. The ectopic overexpression of PavKLUH in Arabidopsis increased the size of its siliques and seeds, whereas virus-induced gene silencing of PavKLUH in sweet cherry significantly decreased fruit size by restricting mesocarp cell expansion. We screened out an AP2/ERF transcription factor containing a B3-like domain, designated as PavRAV2, which was able to physically interact with PavKLUH promoter in a yeast one-hybrid (Y1H) system. In Y1H assays, electrophoretic mobility shift assays, and dual-luciferase reporter analyses, PavRAV2 directly bound to the promoter of PavKLUH in vitro and in vivo, and suppressed PavKLUH expression. Silencing of PavRAV2 resulted in enlarged fruit as a result of enhanced mesocarp cell expansion. Together, our results provide new insights into signaling pathways related to fruit size, and outline a possible mechanism for how the RAV transcription factor directly regulates CYP78A family members to influence fruit size and development.

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